5I4D

1.75 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus, in Complex with Sialyl-LewisX.

• PDB DOI: https://doi.org/10.2210/pdb5I4D/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-11 Released: 2016-02-24 
• Deposition Author(s): Minasov, G., Nocadello, S., Shuvalova, L., Filippova, E.V., Halavaty, A., Dubrovska, I., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.202 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 

Starting Model: experimental

Literature

1.75 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus, in Complex with Sialyl-LewisX.

Minasov, G., Nocadello, S., Shuvalova, L., Filippova, E.V., Halavaty, A., Dubrovska, I., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.79 kDa 
• Atom Count: 4,379 
• Modelled Residue Count: 385 
• Deposited Residue Count: 686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superantigen-like protein	A, B	343	Staphylococcus aureus	Mutation(s): 0  Gene Names: set9, ERS445052_00332, RL02_05830
UniProt
Find proteins for Q2G0X7 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G0X7  Go to UniProtKB:  Q2G0X7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose	C, D	4		N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	F [auth A], H [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900122	C, D	Sialyl-Lewis X antigen, alpha anomer	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.202 
• R-Value Work: 0.161 
• R-Value Observed: 0.163 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/m35i4d

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.975	α = 90
b = 166.881	β = 90
c = 34.144	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Minasov, G., Nocadello, S., Shuvalova, L., Filippova, E.V., Halavaty, A., Dubrovska, I., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary